diff --git a/.gitignore b/.gitignore index 3cb3963..3bbfb9d 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,7 @@ dist testfiles target lib +.settings +src/log4j.properties +.project +.classpath \ No newline at end of file diff --git a/pom.xml b/pom.xml index 4eaaa66..ba08d03 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ de.unirostock.sems BiVeS jar - 1.9.2 + 1.10.0 BiVeS BiVeS - BioModel Version Control System @@ -36,17 +36,17 @@ de.unirostock.sems BiVeS-SBML - 1.7.5 + 1.8.0 de.unirostock.sems BiVeS-CellML - 1.6.6 + 1.7.1 de.unirostock.sems BiVeS-Core - 1.7.2 + 1.8.1 commons-cli @@ -58,6 +58,12 @@ log4j 1.2.17 + + de.unirostock.sems + BiVeS + 1.9.1 + provided + http://mvn.sems.uni-rostock.de diff --git a/src/main/java/de/unirostock/sems/bives/Executer.java b/src/main/java/de/unirostock/sems/bives/Executer.java index 3b329fb..012b147 100644 --- a/src/main/java/de/unirostock/sems/bives/Executer.java +++ b/src/main/java/de/unirostock/sems/bives/Executer.java @@ -81,6 +81,9 @@ public class Executer public static final String REQ_WANT_REACTIONS_DOT = "reactionsDot"; public static final String REQ_WANT_REACTIONS_DOT2 = "crnDot"; + /** The Constant REQ_WANT_REACTIONS_SBGN_JSON. */ + public static final String REQ_WANT_REACTIONS_SBGN_JSON = "reactionsSbgnJson"; + /** The Constant REQ_WANT_REACTIONS_JSON. */ public static final String REQ_WANT_REACTIONS_JSON = "reactionsJson"; public static final String REQ_WANT_REACTIONS_JSON2 = "crnJson"; @@ -188,6 +191,7 @@ private void fillOptions () options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_GRAPHML).desc ("get the highlighted reaction network encoded in GraphML").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_DOT).desc ("get the highlighted reaction network encoded in DOT language").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_JSON).desc ("get the highlighted reaction network encoded in JSON").build ()); + options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_SBGN_JSON).desc ("get the highlighted reaction network encoded in an SBGN-JSON format").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_GRAPHML2).desc ("get the highlighted reaction network encoded in GraphML (deprecated version)").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_DOT2).desc ("get the highlighted reaction network encoded in DOT language (deprecated version)").build ()); options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_JSON2).desc ("get the highlighted reaction network encoded in JSON (deprecated version)").build ()); @@ -509,6 +513,17 @@ else if ((type & DocumentClassifier.XML) != 0) errors.add (e); } + if (line.hasOption (REQ_WANT_REACTIONS_SBGN_JSON)) + try + { + hasOption = true; + toReturn.put (Executer.REQ_WANT_REACTIONS_SBGN_JSON, result (diff.getReactionsSbgnJsonGraph ())); + } + catch (Exception e) + { + errors.add (e); + } + if (line.hasOption (REQ_WANT_COMP_HIERARCHY_DOT)) try {